Protectors of the Universe
by Berserkerlord
Summary: During the excavation on Eden Prime they didn't just find the beacon. They also found two cryogenic pods, inside were two beings who would change the universe.
1. Hiding and Discovery

Disclaimer: Mass Effect and Naruto are the properties of their respective owners.

I recently got Mass Effect 1 and 2, and after searching around I found some pretty good Naruto and Mass effect crossover stories so I thought I would try my hand at it.

So without further adieu here we go.

**AN: Just so we're clear I suck at first chapters so just hang in there the next one should be better.**

* * *

Eden Prime, as humans would call it in many years, was a peaceful idyllic world. The key word in that sentence is "was" because it currently is having the ever-loving shit bombed out of it.

In an underground tunnel only dimly lit by emergency lighting, two figures in gray cloaks paused as the ceiling above them shook with the impact of bombs.

"We have to hurry, soon they'll bring the whole place down on us!" One of the figures said. The figure's companion nodded wordlessly and they continued to rush down the hallway.

They eventually reached their destination, an unmarked metal door. One of the cloaked figures pressed its palm against a scanner next to the door, after a few seconds the door slid open and the two were greeted by a welcome sight, two cryogenic containment pods. The two shared a glance and nodded at each other, before they each stepped into one of the pods. As the doors sealed shut they both immediately felt a drop in temperature as their organs began to slow. They both began to fall into their cryogenically induced sleep, hoping that their hiding place would not be discovered.

* * *

MANY YEARS IN THE FUTURE

* * *

Dr. Warren walked through the scattered Prothean ruins on the surface of Eden Prime. Recently they had unearthed a very important artifact, a Prothean beacon, if they could access the secrets of the beacon then the entire galactic community would benefit. However, after they had discovered the beacon they made another discovery. The beacon had been sitting on top of a large sealed metal room. She was currently headed to this room to witness its opening.

"Doctor, you got here just in time, we were going to open it without you." One of the workers said jokingly.

"Well then it's a good thing I made it here when I did. Proceed." She responded.

The worker nodded and he signaled to several other workers who were standing by the door. They then started to pry the door open, they eventually managed to open it, and suddenly there was a blast of cold air that came out of the room.

One of the workers poked his head inside. "Uh, doctor, I think your going to want to see this." He said in a stunned voice.

"Why? What is it…" Her voice trailed off when she got close enough to see what was inside. Inside of the room were to cryogenic freezing pods, but that wasn't what was important. What was important was the fact that there were two figures inside of them. They were obscured by frost that had accumulated on the glass and when she wiped it away she saw that their features were obscured by cloaks.

One of the crewmen raised an omnitool and his eyes widened when the results were displayed. "Doctor…according to these readings whatever is in there…is still alive." He said, his voice seeming to fail him, and she couldn't blame him.

"We have to secure these pods, these two may be the only survivors of the Prothean race." She said, causing the crew to snap out of their daze. They quickly set about their work, trying to find a way to move the two frozen beings. Oh if only she knew.

* * *

Okay, yeah I know the whole "Naruto is frozen" thing has been done to death, but considering that the Protheans actually tried to suspend themselves it's not that hard to believe.

And in case you couldn't tell there will be an OC in this story.


	2. Hearing and Awakening

Disclaimer: I don't own Mass Effect or Naruto

Remember: Review or the kitty gets it!

* * *

I am aware of the events of Mass Effect 3: From Ashes (thank you internet), but this is not taking place in the third game (Partially because I have only recently received the first two). It will start in the first game and go from there. Just wanted to make that absolutely clear.

I'll be using the default female character for Shepard.

* * *

_There is no problem in the universe that cannot be solved by waving a sufficiently large weapon in someone's face._

* * *

Commander Jane Shepard, survivor of the massacre of her squad on Akuze, and decorated soldier of the Systems Alliance, was currently unconscious in the medical bay of the SSV Normandy. She and the rest of the crew of the Normandy had been sent to pick up an unearthed Prothean beacon on the colony world of Eden Prime. She was also supposed to be observed by a Turian Spectre named Nihlus because she had the potential to become the first human Spectre in history. However, on their approach to Eden Prime they picked up a transmission showing an unidentified ship attacking the colony. She had been sent out with lieutenant Alenko and private Jenkins to try and secure the beacon. Unfortunately two drones killed Jenkins. The two later joined forces with gunnery chief Ashley Williams who had survived an ambush. Williams identified the attackers as Geth, an intelligent race of machines who had not been seen for centuries. After rescuing two scientists who informed them that the beacon had been moved they began to make their way to the spaceport. However when they got there they found the dead body of Nihlus, who had gone ahead to scout. They learned from a worker that he Nihlus been shot by another Turian named Saren. They then followed Saren, who had taken a shuttle to another part of the port, and found several Geth setting explosive charges. They managed to disarm the charges, but when they found the beacon Saren was nowhere to be seen. The beacon seemed to be activated and they called for the Normandy to come retrieve it, however the beacon seemed to start drawing in Ashley, so Jane pushed her out of the way. The beacon then suspended her in mid-air and after several seconds it exploded, sending her crashing to the ground. This is how she found herself lying prone on one of the med bay beds and having strange visions of synthetic life forms slaughtering organics.

* * *

"Doctor, Doctor Chakwas, I think she's waking up." These were the first words that Jane heard as she regained consciousness. She recognized the voice as that of Ashley Williams. She sat up in her bed to see the gray heard doctor standing in front of her.

"You gave us quite the scare commander. How are you feeling." Doctor Chakwas asked.

"Minor throbbing, nothing serious. How long was I out." Jane asked as she rubbed her head.

"About fifteen hours, something happened down there with the beacon." Doctor Chakwas explained.

"It's my fault. I must have triggered some kind of security field when I approached it. You had to push me out of the way." Ashley explained, feeling responsible for the commander's injury.

"You had no way to know what would happen." Jane said, knowing that it wasn't Ashley's fault.

"In fact we don't know what set it off at all, and know it seems we may never know." Doctor Chakwas said.

"The beacon exploded. A system overload, maybe. The blast knocked you out cold. The Lieutenant and I carried you back here to the ship." Ashley explained.

"I appreciate it." Jane said with a smile.

"Physically you're fine, but I did detect some abnormal brain waves. I also noticed an increase in your rapid eye movement, signs typically associated with intense dreaming." Doctor Chakwas said as she crossed her arms.

"I'm not sure what I saw. Nothings really clear." Jane said.

"Well I'd better put that on my report I-oh, Captain Anderson." Doctor Chakwas said noticing as the captain entered the room, causing both Ashley and Jane to stand up and salute.

"How's our XO doing?" Anderson asked Doctor Chakwas.

"She's doing remarkably well, she should be back in service in no time." Chakwas said as she checked a small hand held computer.

"Well if you don't mind I would like to speak to the commander in private." Anderson said.

"Yes, sir. I'll be in the mess if you need me." Ashley said as she walked out.

"And I had better check on our two new visitors." Chakwas said as she followed Ashley out of the room. The mention of "visitors" made Jane curious, from what she had seen none of the survivors had been seriously injured, so just who were these visitors and why did the need the doctors attention?

"Sounds like that beacon hit you pretty hard, Commander. You sure you're okay?" Anderson's voice snapped Jane out of her mental musings.

"I don't like soldiers dying under my command." Jane said, remembering how the geth drones had killed private Jenkins.

"Jenkins wasn't your fault. You did all that you could, Shepard." Anderson said. He knew that ever since her squads death on Akuze Shepard had taken any death under her command very seriously.

"What's so important we needed to talk in private Captain?" Jane asked.

"I'm not going to lie to you, Shepard. Things look bad. Nihlus is dead. The beacon was destroyed and the geth are invading. The Council's going to want answers." Anderson said, not wanting Shepard to get in trouble.

"I didn't do anything wrong Captain. Hopefully the Council can see that." Jane said.

"I'll stand by you Shepard, you're a damned hero in my books. But it's Saren I'm worried about." Anderson said as he began pacing. "Saren's a Spectre, one of the best, he's practically a living legend. But if he's working with the geth, that means he's gone rogue. A rogue Spectre's trouble. Saren's dangerous. And he hates humans." Anderson finished as he came to a stop in front of Jane.

"He didn't come to Eden Prime because he hates humans." Jane said.

"You're right, he's allied himself with the geth. I don't know how, and I don't know why, but he was using them to try and get that beacon. You were there just before the beacon self-destructed. Did you see anything? Any clue that might tell us what Saren was after?" Anderson asked.

"Just before I lost consciousness I had some kind of vision." Jane said as she leaned back on the medical bed.

"A vision? A vision of what?" Anderson asked.

"I saw synthetics. Geth maybe, slaughtering people." Jane said, inwardly shaking as she remembered the sight of people being slaughtered.

"What are we going to tell them? That I had a bad dream." Jane asked, she knew of the Council's distrust of humans.

"Who knows what was inside that beacon, information, blueprints for some kind of ancient weapon of mass destruction? Either way Saren now has the secrets from that beacon. He has an army of geth at his command. And he won't stop until he's wiped humanity from the face of the galaxy!" Anderson said, remembering his own experiences with Saren.

"I'll find some way to take him down." Jane said with resolve in her voice.

"It's not that easy." Anderson sighed. "He's a Spectre. He can go anywhere, do almost anything. That's why we need the Council on our side." He continued.

"We prove Saren's gone rogue and the Council will revoke his status." Jane said as she realized the Captain's plan.

"Exactly, I'll go set up a meeting with the ambassador and see if we can get an audience with the council." Anderson said. "But first we're going to need to wake up our two new visitors." He said.

"The doctor mentioned something about visitors too, what was she talking about?" Jane asked.

"Apparently after they discovered the beacon the researchers discovered two stasis pods in a sealed room underneath the beacon. They weren't able to report there discovery before the geth attack so it no one knew about it except for them, we managed to pick up the stasis pods and doctor Chakwas is trying to determine the status of the two beings inside of them. This could potentially be an even bigger discovery than the beacon, those two pods might contain the last living Prothean's." Anderson said, Jane could hear the excitement in his voice. "I'm off to call the ambassador, I suggest you take a look at the pods before going to Joker in the bridge, we should be reaching the Citadel soon, the pods are down in the cargo bay." Anderson said as he left the room.

Jane left the med bay and found Ashley waiting outside in the mess hall with Kaidan. After telling the two about the pods they decided to go together down to the cargo bay, which was were the pods were being stored. They found Doctor Chakwas scurrying between the two pods, taking readings on the two figures in the pods.

"Hey, Doctor, any idea if those things will be waking up soon?" Kaidan asked as he tapped the glass on one of them.

"No, and don't tap the glass Kaidan, these are finely crafted machines meant to preserve life you shouldn't be so reckle-" The Doctor was cut short as several lights on the machines began to flash.

"Uh, I didn't do that." Kaidan said as he stepped back from the pods. Doctor Chakwas, Jane, and Ashley all followed suit as the lights began to flash with increased rapidity and the glass on the pods began to slide open.

Both of the figures, each wearing heavy cloaks that covered their entire bodies, stumbled out of the pods they looked up at the group assembled before them before looking at each other. One of them then fell to the ground.

Doctor Chakwas rushed over to the figure, only to find her path blocked by the other cloaked figure. It held out one hand, bringing the doctor to a stop, she didn't know if this figure was a biotic, and if it was then a single flick of its wrist could send her flying.

"Please let me pass, I'm a doctor if your friend is hurt then I can help him." She said. The figure, not understanding her language but apparently capable of telling that she would not do his companion harm let her pass. She removed the cloak from the fallen form causing everyone to gasp.

He, for it was most definitely a male, appeared to be human at first glance, but on a second look they realized that he had to fox like ears on the top of his head and a fox tail sticking out from his lower back, his tail, ears, and hair were a bright golden color, his hair was spiky and pointed out in all directions. He also had what appeared to be whisker marks on his face. He was wearing dark red combat armor under the cloak, it gave him an appearance that made it look like his armor was covered in blood.

"I'll need to take him to the med-bay will you allow me?" Chakwas asked the figures companion. He nodded, understanding that she wanted to take his companion somewhere.**(AN: He doesn't understand her language but understands that she doesn't mean any harm, got it?)** Chakwas signaled for Kaidan and Ashley to come and pick up the strange being. She then had them take him to the med bay, with the still cloaked figure and Jane following close behind. When they had him placed on one of the tables she did a full scan on him, when she got the readings she took out a small red capsule from a bottle and made the blonde swallow it, his breathing became slower and steadied.

"What was wrong with him doctor." Jane asked, curious as to what this creature was and why it had collapsed.

"I think it was just from fatigue, the pod probably forced his organs to all but stop functioning and then when it reawakened him it forced his organs to go start working at full capacity again, in fact I'm surprised that his friend here didn't collapse as well." She said, when they turned to look at the other cloaked figure they found him lying on the floor as well.

"It must have taken longer to set in for him I guess." Doctor Chakwas said as Kaidan and Ashley pulled the other figure onto one of the other beds. When they removed his cloak they were shocked to find that he bore little resemblance to the other being. Or at least, from what they could see he didn't look similar.

He had a mask made of gray metal covering his entire head, without any holes for eyes or a mouth, he also wore a similar type of body armor except his was dull gray, the same shade as his mask. Although when they checked, under him they could find no evidence of a tail. When they tried to remove the armor and mask they found that they couldn't move it, no matter how hard they tried. Eventually they gave up, and left the two in the care of doctor Chakwas.

They headed to the bridge to see how Joker was doing.

"Good timing guys, I was just about to bring us into the Citadel, see that taxpayer money at work." Joker said as they came into sight of the Citadel.

"Look at that ship." Ashley said as they caught sight of a massive ship many times bigger than the Normandy.

"It's the ascension, flagship of the Citadel fleet." Kaidan said.

"Yeah, well size isn't everything." Joker said as he looked at the massive ship, unimpressed.

"Why so touchy Joker?" Ashley teased, causing Jane and Kaidan to suppress a snicker.

"I'm just saying you need firepower too." Joker retorted.

"Are you kidding me, that thing could tear through any ship in the Alliance fleet." Ashley argued.

"Then it's a good thing its on our side." Kaidan said, Jane silently agreed with him, she did not want to be on the business end of that ship's massive gun.

"This is the SSV Normandy requesting permission to land." Joker said as he established contact with the tower.

"You're clear Normandy, transferring you to an Alliance operator." Said the voice on the other end of the transmission. Joker took the Normandy in and landed it at one of the docking bays.

Kaidan, Ashley and Jane were leaning over the balcony looking at the scenery while Udina, the human ambassador, argued with the council about how they weren't helping the humans. Jane only snapped to attention when she heard the link cut off and Udina move over to face them.

"Captain Anderson, it seems that you've brought half your crew with you." The ambassador said.

"These were the ones that were on the ground, I thought that it was important for them to be here." Anderson said, the tension between the Captain and the Ambassador was palpable.

"The Council is not happy about those mission reports. Saren's their top agent. They don't like him being accused of treason." Udina said.

"Saren's a threat to every human colony out there, if the council won't stop him then I will." Jane said.

"You've done enough Shepard, you've already jeopardized your candidacy for the Spectres. The mission on Eden Prime was a chance for you to prove yourself. Instead Nihlus ended up dead and the beacon was destroyed." Udina said. Jane could feel her contempt for the man rising.

"That was Saren's fault not hers." Anderson interjected.

"Either way we had better hope the C-Sec investigation finds out something, otherwise we're in deep trouble. You can meet us on the top floor of Citadel tower for the hearing, don't be late." Udina said as he and Anderson left.

"And that's why I hate politicians." Ashley said when the door closed behind the two. Kaidan and Jane nodded, both finding Udina to be an untrustworthy man.

"Well, we better not keep the council waiting." Kaidan said as the three headed for the Citadel Tower.

The three eventually found themselves at the top floor of the Citadel tower. They couldn't help but be awestruck as they entered the massive building. However they were interrupted when they saw two Tuians in front of them arguing.

"Saren is hiding something, I know it. Can't you stall them." One of them asked.

"Stall the Council, don't hold you're breath. The investigation is over Garrus, let it go." The other Turian said as he walked off. The first Turian noticed the group and walked over them.

"Commander Shepard? Garrus Vakarian. I was the officer in charge of the C-Sec investigation into Saren." The now identified Garrus said.

"Come across anything I should know." Jane asked.

"Saren's a Spectre most of his actions are classified, I couldn't find anything concrete. But I can tell Saren is up to something, like you humans say, I can feel it in my gut.

"I think the council's ready for us commander." Kaidan said.

"Good luck Shepard, maybe they'll listen to you." Garrus said as he walked off.

The group then walked through the Citadel until they found Captain Anderson.

"The hearing's already started come on." Anderson said as he led Shepard up the stairs.

* * *

Skipping the hearing so I don't have to write all that.

* * *

"It was a mistake bringing you into the meeting Captain, you and him have to much history together." Udina said as he, Anderson and Shepard stood at the foot of the stairs leading to the council chamber.

"I know Saren, the only reason he's working with the geth is to destroy humanity. Every colony we have is at risk. Every world we control is in danger. Even Earth isn't safe." Anderson said.

"We'll need to deal with Saren ourselves." Jane said.

"As a Spectre he's virtually untouchable, we'll need to find a way to prove his treason." Udina said.

"What about Garrus, that C-Sec officer." Kaidan said as he remembered the Turian from before the hearing.

"That's right! He was asking for more time to finish his report. Seems like he was close to finding something on Saren." Ashley said.

"Any idea where we could find him." Jane asked.

"I have a contact in C-Sec who should be able to track him down, his name is Harking. Shepard will handle this Captain, I don't want the Council using your past history with Saren to dismiss any evidence you turn up against him." Udina said.

"I'll take care of it." Jane said.

"Captain, I'll be taking care of some work, come see me in my office later." Udina said as he walked off.

"Harkin's probably getting drunk at Chora's Den. It's a dingy little club in the lower section of the wards." Anderson said, his voice conveying his disgust for having to rely on a drunkard for information.

"Maybe there's another way we could find information about Saren." Jane said.

"You could ask Barla Von. Rumor has it he's an agent for the Shadow Broker, an information dealer. He might know something about Saren. But his information won't come cheap." Anderson said as he recalled several rumors he had heard.

"I should go." Jane said.

"Good luck Shepard, I'll be in the Ambassador's office if you need anything." Anderson said as he walked off. However, before he could there was a ringing noise and he pulled out a portable computer. As he read the message on the computer his eyes widened. "Shepard, Alenko, Williams, you have to get back to the ship." He said as he began to walk quickly towards the door.

"What's wrong Captain?" Aidan asked as the group caught up with him.

"Our guests have woken up." Anderson said, the three soldiers' eyes widened and they quickly broke into a jog as they headed towards the ship's docking bay.

* * *

All right here you go. The dialogue is pretty hard because I'm actually replaying the game to try and get it as accurate as I can.

Remember, review or the kitty gets it!


End file.
